iiinova — where your digital self keeps evolving

Ricardo Henriques @henriqueslab.bsky.social · 14/10/2026

🔬🚀 A head start on your PhD! Two ERC-funded fellowships for Master's graduates at ITQB NOVA, Lisbon: seven months in our lab (Dec 2026 to Jun 2027) to start your research and build a strong 2027 FCT PhD application with us. Apply by 27 Oct 👇 henriqueslab.org/pages/recruitment

Poster split by a diagonal: a fluorescent human cell in cyan and magenta on the left, a laser bench with green, cyan and red light on the right. Start your PhD with us: two fellowships for Master's graduates at ITQB NOVA, 065/BI/2026 (biology) and 066/BI/2026 (engineering). Apply by 27 October.

286

Ricardo Henriques @henriqueslab.bsky.social · 12/10/2026

For quantitative cell biology, the manuscript can carry its own Python or R code. Figures and reported values are rebuilt from the data at every compile, so the text stays in step with the analysis. One command also packages it for arXiv or bioRxiv 👇 rxiv-maker.henriqueslab.org

Rxiv-Maker architecture. Markdown content, Python scripts, R scripts, BibTeX references and YAML metadata feed the Rxiv-Maker processing engine, which builds a LaTeX document and figures, then outputs a publication-ready PDF and an editable Word file.

A Python code block embedded in a Rxiv-Maker manuscript. It loads monthly arXiv submission counts and computes the totals and year span that the manuscript text then quotes, so the numbers update whenever the data change.

261

Ricardo Henriques @henriqueslab.bsky.social · 12/10/2026

🚀 Rxiv-Maker is now peer-reviewed and open access! Write your manuscript in Markdown and get a typeset PDF or an editable Word file, with figures, citations and cross-references numbered for you. Led by Bruno Saraiva, with @guijacquemet.bsky.social's lab 🔬 doi.org/10.1242/jcs.265183

Top of the first page of the published article 'Rxiv-Maker – an automated template engine for streamlined scientific publications' by Bruno M. Saraiva, Rita Carlota, António D. Brito, Iván Hidalgo-Cenalmor, Guillaume Jacquemet and Ricardo Henriques, showing the title, authors and abstract.

39037

Ricardo Henriques @henriqueslab.bsky.social · 09/10/2026

Most of this stuff (including how the makers want us to perceive AI) is very awkwardly concerning

120

Ricardo Henriques @henriqueslab.bsky.social · 22/09/2026

Just back from the Nature Conference on next-gen fluorescence microscopy @tsinghuauniversity.bsky.social. Awesomely organized! Amazing people to hang out with (we missed you @ritastrack.bsky.social )

3170

Ricardo Henriques @henriqueslab.bsky.social · 15/09/2026

We put it to work on antibiotic phenotyping in E. coli and on cell cycle defects in S. aureus DnaA mutants. It grew out of eHooke, our old S. aureus pipeline, now opened up to rods, cocci and whatever else you image. pypi.org/project/napari-mAIcrobe

Four fluorescence micrographs of Escherichia coli in red and blue, each cell marked with a coloured cross showing its predicted class. Panels are labelled Control, Mecillinam, Nalidixic acid and Control, with cell shape differing between the antibiotic treatments.

070

Ricardo Henriques @henriqueslab.bsky.social · 15/09/2026

Led by António Brito and Bruno Saraiva, with Dominik Alwardt, Beatriz de P. Mariz, Sérgio Filipe and @pinholab.bsky.social, at @itqbnova.bsky.social. Built on @napari.org: StarDist, Cellpose and U-Net, plus a retrainable classifier =)

Four panels. A schematic pairs a microscope with a model, then three split micrographs show raw image beside colour-coded segmentation masks: Staphylococcus aureus by SIM with StarDist, Streptococcus pneumoniae by phase contrast with U-Net, and Bacillus subtilis by widefield with U-Net.

160

Ricardo Henriques @henriqueslab.bsky.social · 15/09/2026

🔬🚀 Out now in Communications AI & Computing: mAIcrobe, our open-source napari plugin for high-throughput bacterial image analysis. Segmentation, morphological profiling and cell cycle classification, all in one place 👇 doi.org/10.1038/s44488-026-00022-y

Screenshot of the published article page. Software, Open access, published 15 September 2026. Title: mAIcrobe, an open-source framework for high-throughput bacterial image analysis. Authors: António D. Brito, Dominik Alwardt, Beatriz de P. Mariz, Sérgio R. Filipe, Mariana G. Pinho, Bruno M. Saraiva and Ricardo Henriques. Communications AI & Computing 1, article number 16 (2026), followed by the abstract.

Diagram of the mAIcrobe workflow. Acquisition feeds into segmentation with StarDist, Cellpose and community models, then into morphological profiling and a three-class cell cycle classifier, ending in a feature-space scatter plot with three separated clusters.

24417

Ricardo Henriques @henriqueslab.bsky.social · 21/07/2026

🚀🔬 Can cell shape, signal and movement tell us about a cell's future? #DeepLearning studies now predict cell fate from #microscopy. Together w Rita, @mariodelr.bsky.social, @inesmcunha.bsky.social, @juliettegriffie.bsky.social + @guijacquemet.bsky.social👇 www.preprints.org/manuscript/202607.1414/v1

26526

Ricardo Henriques @henriqueslab.bsky.social · 30/06/2026

Nuclei as constellations 🔭 #NucleiSky aligns microscopy images across modalities and scales by reading nuclei like stars to map between them. Joy to contribute, led by @ivanhcenalmor.bsky.social and @guijacquemet.bsky.social's team. #RxivMaker powered preprint. Check it out!

0206

Ricardo Henriques @henriqueslab.bsky.social · 17/06/2026

🔬🚀 Updated #VLab4Mic preprint. Rebuilt the clathrin models from full-length triskelions, dome+flat lattice toy simulations share a common motif. Wanna see how it looks across microscopy methods? (Thank you for the advice @stefvass.bsky.social) www.biorxiv.org/content/10.64898/2026.06.02.729521v3

0144

Ricardo Henriques @henriqueslab.bsky.social · 10/06/2026

The legendary @guijacquemet.bsky.social at Sigrid Juselius #AI Symposium. "I'm a cell biologist", but then 1/3 of the talk went to mechanistic cell biology, 1/3 algorithmic technology development and 1/3 AI. Gonna get him a decaf... (legend says he's also coming up soon with adaptive microscopy)

0236

Ricardo Henriques @henriqueslab.bsky.social · 10/06/2026

🔬🚀 Preprint update for #VLab4Mic - our super-resolution experiments virtual simulation system. Now installs as one-click desktop app: no Python, no setup, thanks to the magic of the @guijacquemet.bsky.social's lab #LabConstrictor packaging engine www.biorxiv.org/content/10.64898/2026.06.02.729521v2

1154

Ricardo Henriques @henriqueslab.bsky.social · 05/06/2026

This closes a loop we opened with #NanoJSQUIRREL (@superresolusian.bsky.social et al., 2018), which mapped where super-resolution images go wrong relative to a reference. #VLab4Mic comes at it from the other end: predicting what's resolvable from known atomic structure before you even image

000

Ricardo Henriques @henriqueslab.bsky.social · 05/06/2026

Huge thank you to the labs of @christlet.bsky.social, Dylan Owen and @wmarkbates.bsky.social, and to Tayla Shakespeare, who helped us make it happen. #VLab4Mic also heavily uses data from @rcsbpdb.bsky.social, @jonasries.bsky.social and @taraska.bsky.social

141

Ricardo Henriques @henriqueslab.bsky.social · 05/06/2026

🔬🚀 It's out! Run 100s of imaging experiments before touching a microscope. #VLab4Mic reproduces them in silico from PDB/AlphaFold to help you image right first time. From rockstars Damián Martínez & Bruno Saraiva, inaugural preprint of @mariodelr.bsky.social new lab www.biorxiv.org/content/10.6...

33712

Ricardo Henriques @henriqueslab.bsky.social · 15/01/2026

📯👨‍🚀 Calling all #bioimage analysis aficionados. #EZInput is out! We wanted to bring #ImageJ’s capacity to record settings to the #Python ecosystem 🐍. It is a declarative library for generating UIs that just work. Done with @guijacquemet.bsky.social lab arxiv.org/abs/2601.08859 #ScientificComputing

24515

Ricardo Henriques @henriqueslab.bsky.social · 19/12/2025

Check out rxiv-maker.henriqueslab.org/examples/sho... to have a look at the preprints already using #RxivMaker

210

Ricardo Henriques @henriqueslab.bsky.social · 19/12/2025

🚀📰 End-of-year news for #RxivMaker =). Now it generates both #pdf and #docx from #markdown. Docx makes it easier to collaborate on a document for non-markdown users, making it simple to loop between docx and #RxivMaker to a professional-looking #preprint Preprint updated: arxiv.org/abs/2508.00836

1228

Ricardo Henriques @henriqueslab.bsky.social · 19/12/2025

🧬 @itqbnova.bsky.social has 15 BRIDGE fellowships for Master's graduates pursuing PhDs! We have a spot: "Decoding the morphological language of infection using AI". Build AI to map how viruses hijack cells & bacteria survive antibiotics. Deadline: 05/01/2026 www.itqb.unl.pt/education/br...

031

Ricardo Henriques @henriqueslab.bsky.social · 15/12/2025

Going through my UCL-times photos, this little one came up

1230

Ricardo Henriques @henriqueslab.bsky.social · 15/12/2025

🚨🔬🤖🚀 #PhotoFiTT is out! With @guijacquemet.bsky.social's & @microbematos.bsky.social's labs, we launched a new phototoxicity measurement for live microscopy using cell clocks⏱️. By rockstars @mariodelr.bsky.social @gomez-mariscal.bsky.social et al! AI-powered + label-free doi.org/10.1038/s414...

53411

Ricardo Henriques @henriqueslab.bsky.social · 04/11/2025

Come! We're hosting a fantastic list of speakers and hands-on workshops #ims2026

073

Ricardo Henriques @henriqueslab.bsky.social · 03/11/2025

🔬🤖 ICYMI: impressive preprint from @owenlabuob.bsky.social tackling a major bottleneck – how to systematically compare super-resolution microscopy across experiments. Novel ML framework embeds single-molecule data for cross-sample analysis. Integrated with nano-org database✨ doi.org/10.1101/2025...

0134

Ricardo Henriques @henriqueslab.bsky.social · 28/10/2025

Using #LLMs for science👨‍💻💬? We have a fun tool for you: introducing #folder2md4llms. It converts an entire folder of docs/code/pdfs/pptx into a single markdown file that you can upload to your chatbot of choice. We use it to talk with our publications database or code repos github.com/HenriquesLab...

1196

Ricardo Henriques @henriqueslab.bsky.social · 27/10/2025

🦠🔬🤖🧑‍💻 #mAIcrobe interface preview, a platform for #DeepLearning enabled bacterial image-based phenotyping. Check it out 💻: github.com/HenriquesLab... 📄: www.biorxiv.org/content/10.1...

0359

Ricardo Henriques @henriqueslab.bsky.social · 23/10/2025

Cool news about #RxivMaker. Adding lots of new features 🏃. An rxiv-markdown manuscript can now have embedded code that helps keep all your data updated (e.g. inserting number of samples by reading data like .xls). Both #RxivMaker and #mAIcrobe preprints are written with it arxiv.org/abs/2508.00836

070

Ricardo Henriques @henriqueslab.bsky.social · 22/10/2025

🦠🔬🤖🧑‍💻 #mAIcrobe is out! With @pinholab.bsky.social's lab, we launched an open-source framework for high-throughput bacterial image analysis. By rockstars A. Brito & B. Saraiva et al, making #DeepLearning for phenotyping accessible! Easy to use, plus model training 📜 www.biorxiv.org/content/10.1...

56230

Ricardo Henriques @henriqueslab.bsky.social · 21/10/2025

🚀🔬 Announcing #IMS2026 at @itqbnova.bsky.social! We're assembling a #LifeSciences #Microscopy symposium packed with ✨ speakers and 🧑‍🔬 workshops. All about imaging cells with photons, electrons and AI! If you love microscopy, you need to be here. Join us on March 19! ims2026.itqbnovacommunity.org

12416

Ricardo Henriques @henriqueslab.bsky.social · 15/07/2025

📝 #RxivMaker updated to v1.3.0, new: 🔍 PDF change tracking - see manuscript diffs directly in PDF 🚀 Docker engine in Google Colab & Github Actions = 5x faster installation 🐱 Repo: github.com/HenriquesLab... 📰: zenodo.org/records/1591...

0221

Ricardo Henriques @henriqueslab.bsky.social · 10/07/2025

🚨Join us! We're soon opening 3 postdoctoral positions in #AIDrivenBiology. Seeking biologists (especially microbiology and infection biology), computer scientists, and microscopy developers. Ideal candidates are those eager to use or develop next-gen tech for cell biology. Get in touch (DM/email)

15031

Ricardo Henriques @henriqueslab.bsky.social · 09/07/2025

Scientific coders 🧑‍🔬🧑‍💻 #RxivMaker v1.2 now has a #VSCode extension to manage citations and for syntax highlighting of #RxivMarkdown 💽: github.com/HenriquesLab... 📰: doi.org/10.5281/zeno...

0103

Ricardo Henriques @henriqueslab.bsky.social · 04/07/2025

#RxivMaker updated to v1.1.0: now supports R auto-generated figures and lots of bug fixes Details in: github.com/HenriquesLab...

191

Ricardo Henriques @henriqueslab.bsky.social · 04/07/2025

Hi Bianca, we've added support for generating R figures. Thank you for suggesting it =). If you get a chance to give it a try in the future, let us know how it worked out

110

Ricardo Henriques @henriqueslab.bsky.social · 03/07/2025

It's here! ✨ The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF ➡️ Open link: rdcu.be/euvEw

04315

Ricardo Henriques @henriqueslab.bsky.social · 02/07/2025

Plus, #SReD works on any microscopy images, from fluorescence to electron microscopy 🌐

140

Ricardo Henriques @henriqueslab.bsky.social · 02/07/2025

We follow this up by detecting HIV viral morphogenesis 🦠✨ in live-cell fluorescence images. Leveraging the brilliant expertise of João Mamede’s team

141

Ricardo Henriques @henriqueslab.bsky.social · 02/07/2025

The new #SReD paper is packed with eye-opening demos! We demonstrate how SReD accurately detects spectrin ring patterns in neurons🧠, pinpointing instances where rings are disrupted. Possible through the deep system expertise from @christlet.bsky.social and team!

183

Ricardo Henriques @henriqueslab.bsky.social · 02/07/2025

🔬👨‍💻📰 #SReD is out! Automated structural detection for #ImageJ & #FIJI, from nano to macro ✨🐘. No training data, no bias - texture analysis with GPU acceleration!⚡️ Brainchild of @afonsomendes92.bsky.social and adventure w @christlet.bsky.social lab + friends. Check: www.nature.com/articles/s41...

311041

Ricardo Henriques @henriqueslab.bsky.social · 27/06/2025

So... have a read of our #preprint about #preprints, which makes more #preprints! Kudos to amazing Bruno Saraiva and @guijacquemet.bsky.social, who teamed up to create #RxivMaker and made it awesome

042

Ricardo Henriques @henriqueslab.bsky.social · 27/06/2025

Got 2 minutes to spare and a Google account? Give it a go in Google Colab or fork the repo – everything's been designed to be super easy, with no specialist knowledge needed Colab: colab.research.google.com/github/Henri... Github: github.com/HenriquesLab...

111

Ricardo Henriques @henriqueslab.bsky.social · 27/06/2025

For those of you who use our HenriquesLab #bioRxiv template on @overleaf.com (🙏), the PDFs will look familiar. We enhanced the template with a fully automated, reproducible workflow, building on the style you love Btw, Overleaf is awesome; we've done nearly-all preprints there. You should use it!

131

Ricardo Henriques @henriqueslab.bsky.social · 27/06/2025

Under the #RxivMaker hood: - 🦾 You Write, It Builds: Write #Markdown and engine autogenerates #LaTeX PDF - 📊 Dynamic Figures: Generate figures with #Python or #Mermaid that automatically update when data changes - 🤖 Zero-Install: Runs on #GoogleColab or builds with #GitHub Actions, no local setup

193

Ricardo Henriques @henriqueslab.bsky.social · 27/06/2025

🧑‍🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab 📜: zenodo.org/records/1575... 👨‍💻: github.com/HenriquesLab...

38334